include/dai/evidence.h

   1 /*  Copyright (C) 2009  Charles Vaske  [cvaske at soe dot ucsc dot edu]
   2     University of California Santa Cruz
   3
   4     This file is part of libDAI.
   5
   6     libDAI is free software; you can redistribute it and/or modify
   7     it under the terms of the GNU General Public License as published by
   8     the Free Software Foundation; either version 2 of the License, or
   9     (at your option) any later version.
  10
  11     libDAI is distributed in the hope that it will be useful,
  12     but WITHOUT ANY WARRANTY; without even the implied warranty of
  13     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14     GNU General Public License for more details.
  15
  16     You should have received a copy of the GNU General Public License
  17     along with libDAI; if not, write to the Free Software
  18     Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
  19 */
  20
  21
  22 /// \file
  23 /// \brief Defines classes Evidence and SampleData
  24 /// \todo Improve documentation
  25
  26
  27 #ifndef __defined_libdai_evidence_h
  28 #define __defined_libdai_evidence_h
  29
  30
  31 #include <istream>
  32 #include <dai/daialg.h>
  33
  34
  35 namespace dai {
  36
  37
  38 /// Stores a set of observations on a graphical model.
  39 class SampleData {
  40     private:
  41         std::string _name;
  42         std::map<Var, size_t> _obs;
  43     public:
  44         /// Construct an empty object
  45         SampleData() : _name(), _obs() {}
  46         /// Set the name of the sample
  47         void name(const std::string& name) { _name = name; }
  48         /// Get the name of the sample
  49         const std::string& name() const { return _name; }
  50         /// Read from the observation map
  51         const std::map<Var, size_t>& observations() const { return _obs; }
  52         /// Add an observation
  53         void addObservation(Var node, size_t setting);
  54         /// Add evidence by clamping variables to observed values.
  55         void applyEvidence(InfAlg& alg) const;
  56 };
  57
  58
  59 /// Store observations from a graphical model.
  60 class Evidence {
  61     private:
  62         std::map<std::string, SampleData> _samples;
  63 public:
  64     /// Start with empty obects, then fill with calls to addEvidenceTabFile()
  65     Evidence() : _samples() {}
  66
  67     /** Read in tab-data from a stream. Each line contains one sample, and
  68      *  the first line is a header line with names. The first column contains
  69      *  names for each of the samples.
  70      */
  71     void addEvidenceTabFile(std::istream& is, std::map< std::string, Var >& varMap);
  72
  73     /** Read in tab-data from a stream. Each line contains one sample,
  74      *  and the first line is a header line with variable IDs. The first
  75      *  column contains names for each of the samples.
  76      */
  77     void addEvidenceTabFile(std::istream& is, FactorGraph& fg);
  78
  79     /// Total number of samples in this evidence file
  80     size_t nrSamples() const { return _samples.size(); }
  81
  82     /// @name iterator interface
  83     //@{
  84     typedef std::map< std::string, SampleData >::iterator iterator;
  85     typedef std::map< std::string, SampleData >::const_iterator const_iterator;
  86     iterator begin() { return _samples.begin(); }
  87     const_iterator begin() const { return _samples.begin(); }
  88     iterator end() { return _samples.end(); }
  89     const_iterator end() const { return _samples.end(); }
  90     //@}
  91 };
  92
  93
  94 } // end of namespace dai
  95
  96
  97 #endif